Mr. Epstein, 44, author of the book “Good Without God,” is a seemingly unusual choice for the role. He will coordinate the activities of more than 40 university chaplains, who lead the Christian, Jewish, Hindu, Buddhist and other religious communities on campus. Yet many Harvard students — some raised in families of faith, others never quite certain how to label their religious identities — attest to the influence that Mr. Epstein has had on their spiritual lives.

“There is a rising group of people who no longer identify with any religious tradition but still experience a real need for conversation and support around what it means to be a good human and live an ethical life,” said Mr. Epstein, who was raised in a Jewish household and has been Harvard’s humanist chaplain since 2005, teaching students about the progressive movement that centers people’s relationships with one another instead of with God.

To Mr. Epstein’s fellow campus chaplains, at least, the notion of being led by an atheist is not as counterintuitive as it might sound; his election was unanimous.